Merge pull request #39 from ccb-hms/development

Update dependencies and command-line interface

requirements.txt

@@ -1,15 +1,15 @@
-Owlready2==0.40
-argparse==1.4.0
-pandas==1.5.3
-numpy==1.24.2
-gensim==4.3.0
-scipy==1.10.1
-scikit-learn==1.2.1
-setuptools==67.6.0
-requests==2.28.2
-tqdm==4.65.0
-sparse_dot_topn==0.3.4
-bioregistry==0.6.92
-nltk==3.8.1
-rapidfuzz==2.13.7
-shortuuid==1.0.11
+Owlready2~=0.44
+argparse~=1.4.0
+pandas~=2.0.3
+numpy~=1.24.2
+gensim~=4.3.0
+scipy~=1.10.1
+scikit-learn~=1.2.1
+setuptools~=67.6.0
+requests~=2.31.0
+tqdm~=4.66.1
+sparse_dot_topn~=0.3.4
+bioregistry~=0.10.6
+nltk~=3.8.1
+rapidfuzz~=2.13.7
+shortuuid~=1.0.11

test/test-pypi.py

@@ -9,8 +9,8 @@ def main():
 			text2term.map_terms(["fever", "headache"], "https://github.com/EBISPOT/efo/releases/download/current/efo.owl")
 			text2term.cache_ontology("https://github.com/EBISPOT/efo/releases/download/current/efo.owl", "EFO")
 			text2term.map_terms(["fever", "headache"], "EFO", use_cache=True)
-			text2term.map_terms(["fever", "headache"], "EFO", base_iris=("www."), mapper=text2term.mapper.Mapper.levenshtein, max_mappings=4, use_cache=True)
-			
+			text2term.map_terms(["fever", "headache"], "EFO", base_iris=("http://www.ebi.ac.uk/efo",), mapper=text2term.mapper.Mapper.LEVENSHTEIN, max_mappings=4, use_cache=True)
+
 			# Properties and classes tests
 			text2term.map_terms(["fever", "headache"], "EFO", term_type="classes", use_cache=True)
 			text2term.map_terms(["contains", "location"], "EFO", term_type="properties", use_cache=True)

text2term/__main__.py

@@ -1,7 +1,8 @@
 import argparse
 import os
 import sys
-from t2t import map_file, cache_ontology, cache_exists
+from t2t import map_terms, cache_ontology
+from onto_cache import cache_exists
 from mapper import Mapper
 
 if __name__ == "__main__":
@@ -56,7 +57,8 @@
     if acronym != "":
         cache_ontology(target, acronym, iris)
         target = acronym
-    map_file(arguments.source, target, output_file=arguments.output, csv_columns=csv_columns,
-                         excl_deprecated=arguments.excl_deprecated, mapper=mapper, max_mappings=arguments.top_mappings,
-                         min_score=arguments.min_score, base_iris=iris, save_graphs=arguments.save_term_graphs,
-                         save_mappings=True, separator=arguments.separator, use_cache=cache_exists(target), term_type=arguments.term_type)
+    map_terms(arguments.source, target, output_file=arguments.output, csv_columns=csv_columns,
+              excl_deprecated=arguments.excl_deprecated, mapper=mapper, max_mappings=arguments.top_mappings,
+              min_score=arguments.min_score, base_iris=iris, save_graphs=arguments.save_term_graphs,
+              save_mappings=True, separator=arguments.separator, use_cache=cache_exists(target),
+              term_type=arguments.term_type)

text2term/config.py

@@ -1 +1 @@
-VERSION = "3.0.1"
+VERSION = "3.0.2"